You — as your collection of 38,000,000,000,000 (38 trillion) microbes — will never be the same as you are in this moment. It’s a fun thought to bring you into the present whenever you need to feel grounded, or when you need a reminder of all that your body (microbes included) does for you.
Knowledge about the human microbiome (this phrase actually refers to a collection of microbiomes in the body) has skyrocketed in recent years. Microbiome research began to take off only two decades ago, thanks to sequencing technologies that emerged from the Human Genome Project, with $1.7 billion spent on research since 2009.
What’s so cool about the world of the micro is that invisibly, it influences your physical, emotional, and mental experience of life. The more we understand it, the greater our ability to change our mood and behavior and to prevent and solve our health problems, on an individual and collective scale.
Only 7% of your microbiome can be explained by inheritance — the rest is shaped by how you live. Our microbiome develops rapidly during the first three years of life, but the factors that shape it during that time, including nutrition, environment (including who we live with!), and antibiotics and antimicrobials, continue to do so at every stage of life.
It may be true that bacteria influence what we look like and how we feel, but it’s also true that we have agency to determine our health journey throughout life.
What Is the Microbiome?
A microbiome is a collection of microorganisms in a specific environment. It includes not only the microorganisms themselves but also their genes, structural elements, metabolites, and surroundings — collectively forming a unique ecosystem. (To allow your inner nerdiness to light you up, as mine often does, read Seed’s Microbiome 101 or tap through Seed University’s stories.)
Technically, a microbiome includes not only bacteria but also fungi (also referred to as the “mycobiome”), viruses (the “virome”), and many other microorganisms. The term “microbiota” refers to just the bacteria themselves.
As you may have guessed, multiple microbiomes exist harmoniously within the body. The gut microbiome is the most well-known, but there are also vaginal, oral, and skin microbiomes. Even your eyes, lungs, and urogenital tract have microbiomes.
The natural world has microbiomes, too, composing a whole other body of research and development that I encourage you to read about but that we won’t cover here.
The Roots of the Microbiome
Scientists, integrative and naturopathic clinicians, and nutritionists are increasingly noting the fact that health starts in the gut.
Fiber 101
In the gut, microbes create short-chain fatty acids and other metabolites when they break down fiber. Fiber is found in all plants, although is present in higher quantities in some plants than in others. Microbes act on soluble fiber (as opposed to insoluble fiber) to produce metabolites.
Viscous fibers allow bacteria to produce metabolites known as short-chain fatty acids. There are many types of short-chain fatty acids, the most abundant of which are:
· Acetate
· Propionate
· Butyrate
Butyrate in particular receives a lot of attention because the body can’t make it on its own — it derives it largely from microbial biochemical reactions — and it’s important! Among its many benefits, it helps to:
· Give energy to the cells composing the gut lining
· Reduce oxidative stress and prevent inflammation by stimulating production of glutathione, your body’s most important antioxidant for detoxification
· Manage the production of regulatory T-cells to defend against pathogens and certain autoimmune conditions, including those involving inflammation of the central nervous system
· Support metabolic health by regulating blood sugar and stimulating production of hormones
Different gut bacteria produce different SCFAs. Interestingly, herbal medicines may also produce SCFAs by modulating the gut microbiota. Berberine, for example, contributes to the production of acetic acid and propionic acid.
Fermentable fibers feed your gut bacteria (they’re also known as prebiotics), positively changing the gut microbiome. They do this by increasing quantities of the protective gut bacteria Bifidobacterium, for example, and by improving your Firmicutes to Bacteroidetes ratio.
Together, these two phyla compose 90% of the gut microbiome. Having more Firmicutes like Lactobacillus is associated with a healthier gut and leaner body type (they also produce butyrate).
3 Roles of the Microbiome
Balanced flora in the gut support balance in the body by interacting with your immune system, brain, and hormones.
The Gut-Immune Axis
You might have heard that you receive your first microbes from your biological mom when you’re born, a process called seeding.
Metabolites produced by maternal microbes, immune cells, and antibodies create the prenatal immune system, allowing newborns to mount an immune response directly after birth, and a baby’s immune system continues to develop throughout the first 2-3 years of life alongside their microbiome. This is one reason it’s so important to protect baby’s microbiome by preventing antibiotic overuse, which can compromise the microbiome and thus immunity.
From our first breaths (and possibly even before we’re born), the relationship between our microbiome and immune system is clear, and there’s even a name for it: the gut-immune axis.
Gut microbes communicate with immune receptors and cells by producing those metabolites noted above. They also maintain proper immune response by:
· Controlling inflammation
· Inducing the release of cytokines and chemokines, which move throughout the circulatory system and lymphatic system (a part of your immune system)
· Reinforcing gut barrier integrity by supporting the presence of tight junctions, intracellular connectors lining your gut (intestinal hyperpermeability can provoke autoimmunity and cause many other symptoms)
· Nudging out pathogens by competing for nutrients and space and producing antimicrobial substances
The Gut-Brain Axis
As someone who used to write for neuroscientists, I may be biased in saying that the gut-brain axis may be a more popularly recognized phrase than the gut-immune axis. All the same, this network of physiological pathways connecting the gut and brain is implicated in many psychological, psychiatric, and neurological disorders, including Alzheimer’s, Parkinson’s, autism, schizophrenia, depression, anxiety, multiple sclerosis, and irritable bowel syndrome (which has recently been recognized as a miscommunication between your brain and gut cells).
Neural, endocrine, and immune communication with the central nervous system is bidirectional and influenced directly by the gut microbiome. Your gut microflora stimulate the release of hormones from what are known as enteroendocrine cells, specialized endocrine cells in the gut (the enteric nervous system is the nervous system in your gut). Enteroendocrine cells also produce neurotransmitters such as serotonin, which makes you feel calm and happy, that can travel to the brain or act on nearby enteric neurons.
The Vagus Nerve
The primary way in which bidirectional communication takes place, however, is via the vagus nerve, which has received a lot of attention within the wellness space for its role in calming the nervous system. (For a primer on polyvagal theory and the twelve cranial nerves, of which the vagus nerve is the tenth, plus exercises to quickly reset your nervous system, read Accessing the Healing Power of the Vagus Nerve by Stanley Rosenberg.)
The vagus nerve comprises both afferent (going to the brain) and efferent (coming from the brain) neurons. In Your Body Is Your Brain, Amanda Blake describes somatic intelligence, or how afferent nerves inform your brain about sensation, suggesting that your brain may not be the know-it-all it thinks it is: “A small group of cells in the amygdala—a tiny bit of brain involved in assessing danger—fires six to eight milliseconds after each heartbeat. The implication: when there’s something to be scared of, your rapidly beating heart lets your brain know.”
Afferent nerves respond to stimuli including nutrients, peptides, hormones, and cytokines, so microbiota can affect signaling to the brain by inducing the release of these factors from enteroendocrine or gastrointestinal immune cells.
By affecting vagus nerve signaling, microbiota may change vagal tone, or the dominance of your parasympathetic nervous system in the dynamic interaction between the parasympathetic (rest and digest) and sympathetic (fight or flight) branches of the autonomic nervous system.
Another topic that’s talked about in the health and wellness community is heart rate variability (HRV). As it turns out, HRV is also a measure of parasympathetic activation, as cardiac vagal tone.
The Gut-Vagina Axis
Over the past two years, my health journey has mostly involved my vaginal microbiome. I wrote about my experience with frequent UTIs and ureaplasma. At the same time as all of that was happening, and for a period of a little over a year after the ureaplasma resolved, I was having vaginal problems too.
They were heart-wrenching and devastating and reduced me to tears, repeatedly. They made me more resilient, taught me how to listen to my body and manage stress when I sense that something is off, and launched my intellectual journey into microbiome sciences.
Considering that the gut microbiome has systemic, whole-body effects, is it possible that connections also exist across microbiomes? For example, could the gut microbiome and vaginal microbiome be linked?
The Estrobolome and Estrogen Metabolism
It’s a fairly new discovery that your gut microbiome changes your hormones. A unique microbiome within your gut microbiome, known as the estrobolome, has special genes that allow these bacteria to metabolize estrogen, a hormone that carries out many important functions in the body.
Once estrogens circulating in the bloodstream have done their job, they wind up in the liver, where the majority of estrogen metabolism takes place. Some estrogens are reabsorbed, while others are destined for removal. Those that travel to the gut are further metabolized by the estrobolome in a process called deconjugation.
Healthy gut function supports hormone balance, and in return, healthy estrogen levels support healthy gut function by maintaining gut barrier integrity; however, you need the right balance of microorganisms in your gut to support healthy estrogen levels.
Some studies have found that an imbalance in certain populations of gut bacteria (which could be caused by taking antibiotics, for example) disrupts the deconjugation process (and decreases urinary estrogens, which suggests a direction for research on the urogenital microbiome).
Hormone Balance and Vaginal Health
In the vagina, estrogen facilitates the growth of lactobacilli — which has a protective effect — by instructing your epithelial cells to produce glycogen, which existing lactobacilli metabolize into lactic acid (CH₃CHCOOH). This reaction creates an acidic environment in the vagina, with pH levels between 3.5 and 4.5, further promoting growth of lactobacilli and inhibiting growth of disruptive bacteria. (Two enantiomers of lactic acid exist, D-lactic acid and L-lactic acid, with D-lactic acid exhibiting more protective effects than L-lactic acid, but both kinds exhibit positive effects.)
In addition, a healthy vagina dominated by Lactobacillus species naturally maintains the integrity of the vaginal epithelial barrier, a physical and immunological barrier. The lactobacilli produce certain proteins and antibodies that prevent pathogens from contacting vaginal epithelial cells and neutralize any antigenic microbial products that look like a threat. Lactic acid also upregulates expression of tight junction proteins in vaginal epithelial cells — your vaginal microbes support the presence of tight junctions, just like in the gut!
The gut microbiome may serve as a reservoir for pathogens that can disrupt your vaginal microbiome, so maintaining the vaginal epithelial barrier is important. Interestingly, the naturopathic doctor I was working with for the UTIs noted on one occasion that we had to “find the reservoir.”
My Inner World
While I wouldn’t wish to repeat the experiences that prompted me to learn about the vaginal microbiome, those experiences and my research have led me to develop a deep respect for the innumerable ways in which the body is intricately connected. They’ve led me to see the world within the human body as one in which chemical messengers can be catalogued and known, with still so much to discover — and a whole other world of biodiversity waiting to be known outside.
This perspective shift feels like a spacious cognizance of all of the ways in which microorganisms are always communicating with the immune system, the brain, the vagina at once, working cohesively to allow us to make love, manage stress, fight infection, and carry out our beautiful lives.